The events that initiate complex inflammatory and autoimmune disorders are largely unknown. In this proposal, we will test a new hypothesis that links metabolic disturbance and the intestinal microbiota with the initiation and/or dysregulation of intestinal immunity. Both the microbiota and metabolic defects have been implicated in immune disorders. The intestinal microbiota, for example, have been implicated in the pathogenesis of inflammatory bowel disease and autoimmune disorders such as type-1 diabetes, and recent clinical trials have suggested that early metabolic defects can be seen children at risk of Diabetes before any clinical signs of disease. Until recently it has been unclear how metabolic disturbances might underlie inflammatory/autoimmune disorders, but a recent discovery in mice suggests that there may be a direct link. Here we propose to characterize this link, and to assess what role the microbiota may play in translating a metabolic defect into an immune response. Mice whose intestinal epithelium is deficient for the transcription factor, GATA4, are defective in certain aspects of intestinal lipid metabolism and have been found to also have dysregulated intestinal immunity. The central hypothesis of this proposal, therefore, is that perturbations in metabolic processes lead to upregulation/dysregulation of immunity through two non-mutually exclusive pathways: 1) a change in the microbiota, caused by the metabolic perturbation, that disrupts the normal intestinal immune balance 2) a direct linkage between metabolic and immune gene networks. In specific aim 1 we will define the full range of gene expression differences between GATA4 deficient and sufficient mice, and then determine whether and how the microbiota may influence these differences. In specific aim 2 we will dissect, in a reductionist model system in vitro, the genes critical for cell intrinsic (microbe-independent) connections between the metabolic and immune networks. This project brings together two internationally recognized PIs, and two rising young systems biologist and microbiologist with unique and complementary expertise in fundamental immunology, intestinal immunity, the microbiome, and autoimmunity. The program described in this application will dissect a hitherto unknown pathway of immune initiation, and dysregulation that may underlie a number of autoimmune and inflammatory disorders.